Covid & Economics Case for Rich & Poor Countries. Advanced Visualizations in R.

1. Introduction and Objectives

In this project we will look at the Covid data from a different perspective. We will analyze data with regards to world economy. We will look at different countries economic parameters and derive some insights. Basically, we would like to answerd questions such as: which countries have more cases poor countries vs rich countries. We will also group countries by continent and look for patterns they may have. Also, we will show visualization that will tell story about covid and economy relationship. In the second part of the analysis, we will introduce foreign exchange rates and we will at it to derive insights. Our hypothesis is that, those countries who have more covid cases, their exchange rate should fall down and have some devaluation problems. We will also observe data for different continents and groups.

2. Data Source

The data is located on GitHub and it is updated constantly by John Hopkins University. The data is directly sources from GitHub and we use live connecion. https://github.com/owid/covid-19-data/tree/master/public/data

Information about Confirmed cases and deaths comes from the COVID-19 Data Repository by the Center for Systems Science and Engineering (CSSE) at Johns Hopkins University (JHU).

Information about Hospitalizations and intensive care unit (ICU) admissions comes from the European Centre for Disease Prevention and Control (ECDC) for a select number of European countries; the government of the United Kingdom; the COVID Tracking Project for the United States; the COVID-19 Tracker for Canada.

Information about Testing for COVID-19 is collected by the Our World in Data team from official reports;

Information about Vaccinations against COVID-19 is collected by the Our World in Data team from official reports.

The benefit of data is that it is constantly updated.

data <- read_csv("https://covid.ourworldindata.org/data/owid-covid-data.csv")

3. Data Description

Data contains 67,439 rows and 59 variables. Data is increasing since an observation is about one country data per day. Therefore, each day the data points are increasing.

glimpse(data)

Rows: 61,486
Columns: 55
$ iso_code                              <chr> "AFG", "AFG", "AFG", "AFG", "...
$ continent                             <chr> "Asia", "Asia", "Asia", "Asia...
$ location                              <chr> "Afghanistan", "Afghanistan",...
$ date                                  <date> 2020-02-24, 2020-02-25, 2020...
$ total_cases                           <dbl> 1, 1, 1, 1, 1, 1, 1, 1, 2, 4,...
$ new_cases                             <dbl> 1, 0, 0, 0, 0, 0, 0, 0, 1, 2,...
$ new_cases_smoothed                    <dbl> NA, NA, NA, NA, NA, 0.143, 0....
$ total_deaths                          <dbl> NA, NA, NA, NA, NA, NA, NA, N...
$ new_deaths                            <dbl> NA, NA, NA, NA, NA, NA, NA, N...
$ new_deaths_smoothed                   <dbl> NA, NA, NA, NA, NA, 0, 0, 0, ...
$ total_cases_per_million               <dbl> 0.026, 0.026, 0.026, 0.026, 0...
$ new_cases_per_million                 <dbl> 0.026, 0.000, 0.000, 0.000, 0...
$ new_cases_smoothed_per_million        <dbl> NA, NA, NA, NA, NA, 0.004, 0....
$ total_deaths_per_million              <dbl> NA, NA, NA, NA, NA, NA, NA, N...
$ new_deaths_per_million                <dbl> NA, NA, NA, NA, NA, NA, NA, N...
$ new_deaths_smoothed_per_million       <dbl> NA, NA, NA, NA, NA, 0, 0, 0, ...
$ reproduction_rate                     <dbl> NA, NA, NA, NA, NA, NA, NA, N...
$ icu_patients                          <lgl> NA, NA, NA, NA, NA, NA, NA, N...
$ icu_patients_per_million              <lgl> NA, NA, NA, NA, NA, NA, NA, N...
$ hosp_patients                         <lgl> NA, NA, NA, NA, NA, NA, NA, N...
$ hosp_patients_per_million             <lgl> NA, NA, NA, NA, NA, NA, NA, N...
$ weekly_icu_admissions                 <lgl> NA, NA, NA, NA, NA, NA, NA, N...
$ weekly_icu_admissions_per_million     <lgl> NA, NA, NA, NA, NA, NA, NA, N...
$ weekly_hosp_admissions                <lgl> NA, NA, NA, NA, NA, NA, NA, N...
$ weekly_hosp_admissions_per_million    <lgl> NA, NA, NA, NA, NA, NA, NA, N...
$ total_tests                           <lgl> NA, NA, NA, NA, NA, NA, NA, N...
$ new_tests                             <lgl> NA, NA, NA, NA, NA, NA, NA, N...
$ total_tests_per_thousand              <lgl> NA, NA, NA, NA, NA, NA, NA, N...
$ new_tests_per_thousand                <lgl> NA, NA, NA, NA, NA, NA, NA, N...
$ new_tests_smoothed                    <lgl> NA, NA, NA, NA, NA, NA, NA, N...
$ new_tests_smoothed_per_thousand       <lgl> NA, NA, NA, NA, NA, NA, NA, N...
$ positive_rate                         <lgl> NA, NA, NA, NA, NA, NA, NA, N...
$ tests_per_case                        <lgl> NA, NA, NA, NA, NA, NA, NA, N...
$ tests_units                           <lgl> NA, NA, NA, NA, NA, NA, NA, N...
$ total_vaccinations                    <lgl> NA, NA, NA, NA, NA, NA, NA, N...
$ new_vaccinations                      <lgl> NA, NA, NA, NA, NA, NA, NA, N...
$ new_vaccinations_smoothed             <lgl> NA, NA, NA, NA, NA, NA, NA, N...
$ total_vaccinations_per_hundred        <lgl> NA, NA, NA, NA, NA, NA, NA, N...
$ new_vaccinations_smoothed_per_million <lgl> NA, NA, NA, NA, NA, NA, NA, N...
$ stringency_index                      <dbl> 8.33, 8.33, 8.33, 8.33, 8.33,...
$ population                            <dbl> 38928341, 38928341, 38928341,...
$ population_density                    <dbl> 54.422, 54.422, 54.422, 54.42...
$ median_age                            <dbl> 18.6, 18.6, 18.6, 18.6, 18.6,...
$ aged_65_older                         <dbl> 2.581, 2.581, 2.581, 2.581, 2...
$ aged_70_older                         <dbl> 1.337, 1.337, 1.337, 1.337, 1...
$ gdp_per_capita                        <dbl> 1803.987, 1803.987, 1803.987,...
$ extreme_poverty                       <dbl> NA, NA, NA, NA, NA, NA, NA, N...
$ cardiovasc_death_rate                 <dbl> 597.029, 597.029, 597.029, 59...
$ diabetes_prevalence                   <dbl> 9.59, 9.59, 9.59, 9.59, 9.59,...
$ female_smokers                        <dbl> NA, NA, NA, NA, NA, NA, NA, N...
$ male_smokers                          <dbl> NA, NA, NA, NA, NA, NA, NA, N...
$ handwashing_facilities                <dbl> 37.746, 37.746, 37.746, 37.74...
$ hospital_beds_per_thousand            <dbl> 0.5, 0.5, 0.5, 0.5, 0.5, 0.5,...
$ life_expectancy                       <dbl> 64.83, 64.83, 64.83, 64.83, 6...
$ human_development_index               <dbl> 0.498, 0.498, 0.498, 0.498, 0...

The datatable sample is shown below.

# data <- read.csv('owid-covid-data.csv', stringsAsFactors = F)
data$date <- as.Date(data$date, "%Y-%m-%d")
knitr::kable(data[1:5, ])

4. Aggregating Data

We will select only important colums such as location, continent, gdp_per_capita, population_density, total_cases, total_cases_per_million, population. This is to use wisely our computation memory and derive useful insights in our graphs. Next step is to remove World and International from the dataset since we will concentrace on countries and those files will be outliers in the graphs.

library(dplyr)
temp <- data.frame(data) %>% dplyr::select(location, continent, gdp_per_capita, population_density, 
    total_cases, total_cases_per_million, population)

temp[is.na(temp)] <- 0

temp <- subset(temp, location != "World" & location != "International")
data_agg <- temp %>% group_by(location, continent) %>% summarise(total_cases = max(total_cases), 
    gdp_per_capita = max(gdp_per_capita), population_density = max(population_density), 
    total_cases_per_million = max(total_cases_per_million), population = max(population))


knitr::kable(data_agg[1:10, ], capture = "Dataset first 10 records")

5. Distributions

Let’s start out analysis with distributions. First of all, let’s observe the distribution of the GDP_per_capita. On the graph we see that the distribution is skewed on the right. The majority of countries have less than 20.000 USD GDP per Capita. Which means that the world has much more poor countries than rich.

library(ggplot2)
library(scales)

ggplot(data_agg, aes(x = gdp_per_capita)) + geom_histogram(aes(y = ..density..), 
    colour = "black", fill = "white") + geom_density(color = "darkblue", fill = "#E69F00", 
    alpha = 0.7) + labs(title = "What is the Distribution of GDP per capita?", subtitle = "Right-skewed distribution, many poor countries") + 
    theme(plot.title = element_text(size = 16, color = "#0B8389", face = "bold"), 
        plot.subtitle = element_text(size = 11)) + scale_y_continuous(labels = comma) + 
    scale_x_continuous(labels = comma)

6. Grouping Countries by Income

Let’s group coutnries in three countries and observe how many countries we have in each group. We will use GDP_per_capita to define the groups rich, medium and poort countries. Countries between 0-7.000 USD GDP_per_capita we call this group “poor”. The countries with GDP_per_capita between 7.000-20.000 USD, we call them “medium” income countries. And the thirds group is countries with GDP_per_capita more than 20.000 USD.

Looking at the graph we see that 40 countries in Africa are in poor countries categories. We definitely do not want the world to have that many poor countries and especially in one continent. The Europe is the continent with many rich countries and only one poor country which is Moldova. North and South America have many Medium income countries. However, our desire is to have evenly distributed wealth in every continent and countries.

library(DT)
data_agg$gdp_per_capita_group <- cut(data_agg$gdp_per_capita, breaks = c(0, 7000, 
    20000, 40000), include.lowest = FALSE, dig.lab = 6)


data_for_dist.a <- data_agg %>% group_by(continent) %>% dplyr::count(gdp_per_capita_group)
data_for_dist.a <- na.omit(data_for_dist.a)

# datatable(head(data_for_dist.a), caption = 'Distribution of countries by
# GDP_per_capita groups & continents')

wrapper <- function(x, ...) {
    paste(strwrap(x, ...), collapse = "\n")
}

ggplot(data_for_dist.a, aes(x = continent, y = gdp_per_capita_group)) + geom_tile(aes(fill = n), 
    color = "white", show.legend = F) + theme_minimal() + geom_text(aes(label = n), 
    size = 5, fontface = "bold", color = "white") + scale_fill_gradient(low = "#6bb0c4", 
    high = "#dd5f64") + theme(panel.grid = element_blank(), plot.title = element_text(size = 16, 
    color = "#0B8389", face = "bold"), plot.subtitle = element_text(size = 11), axis.text.y = element_text(size = 10), 
    axis.text.x = element_text(size = 10)) + ggtitle(wrapper("Distribution of countries by GDP_per_capita groups & continents", 
    width = 60)) + labs(subtitle = wrapper("Moldova in Europe and Bolivia in South America only countries with less than $7,000 GDP_per_capita", 
    width = 80))

7. Rich vs Poor Countries & Covid Cases

Looking at the below graph we want to answer question, Do rich countries have more covid cases? Graph answers that questions as this is true assumptions - rich countries have more covid cases. We think this is due to the fact the in rich countries population is tested massively and also statistic is kept more accurate to count cases than comparing with poor countries. The poor countries do not count cases successfully and even more critical is that they do not test the population as the test are not available for most of them.

library(plotly)
library(ggrepel)

data_agg$population_mln <- as.numeric(data_agg$population/1e+06)
ggplot(data_agg, aes(x = total_cases, y = gdp_per_capita, color = continent, size = population_mln)) + 
    geom_point(alpha = 0.5) + labs(x = "Total Cases", y = "GDP per capita", title = "Where are European countries on the scatterplot?", 
    subtitle = "Just on the top-right, behind the US!", caption = "Date: 2021-Jan-29") + 
    theme(panel.background = element_rect(fill = "white", color = "white", size = 1.2), 
        plot.background = element_rect(fill = "white"), plot.title = element_text(size = 16, 
            face = "bold", color = "#0B8389"), plot.subtitle = element_text(size = 11), 
        plot.caption = element_text(face = "italic", size = 8), panel.grid.major = element_line(linetype = "dashed", 
            size = 0.1), panel.grid.minor = element_blank(), axis.text.y = element_text(size = 10), 
        axis.text.x = element_text(size = 10), legend.position = "bottom") + scale_x_continuous(trans = "log10", 
    labels = comma) + scale_y_continuous(trans = "log10", labels = comma) + scale_size(range = c(0.1, 
    20), name = "Population [mln]") + guides(color = guide_legend(override.aes = list(size = 6)))

# ggplotly(a)

8. Heatmap to show I and II wave of Covid

Below heatmap shows monthly new covid cases for European countries. The Heatmap gives us good demonstration when we have first and the second waves of the corona virus cases spikes. The colors are based on the covid cases. The dark red is a lot of cases while yeallow whiteish is less cases. In the first wave Spain, Italy, Germany and France has a lot of case during March and April in 2020. While during the second wave we see a lot of redish cells during October 2020 and January 2021, especially in the countries such as Spain, Italy, Poland, Germany, France, Belgium and the Netherlands.

library(lubridate)
library(dplyr)

EU <- c("Austria", "Belgium", "Bulgaria", "Croatia", "Cyprus", "Czech Republic", 
    "Denmark", "Estonia", "Finland", "France", "Germany", "Greece", "Hungary", "Ireland", 
    "Italy", "Latvia", "Lithuania", "Luxembourg", "Malta", "Netherlands", "Poland", 
    "Portugal", "Romania", "Slovakia", "Slovenia", "Spain", "Sweden")


data_for_month <- data.frame(data) %>% dplyr::select(location, date, new_cases) %>% 
    filter(location %in% EU)
data <- data.frame(data)

datats <- data.frame(data) %>% dplyr::select(continent, date, total_cases)


data_for_month$month <- floor_date(data_for_month$date, "month")

data_for_month <- as.tibble(data_for_month) %>% group_by(location, month) %>% summarize(new_cases = as.numeric(sum(new_cases)))

data_for_month$month <- as.character(data_for_month$month)
data_for_month$new_cases_1000 <- as.numeric(data_for_month$new_cases/1000)
ggplot(data_for_month, aes(month, location)) + geom_tile(aes(fill = new_cases_1000), 
    colour = "white") + labs(title = "Which month had the biggest amount of new cases?", 
    subtitle = "First wave in Mar 2020 and the second wave in Sep-Oct 2020!", caption = "Date: 2021-Jan-29") + 
    scale_x_discrete("", expand = c(0, 0)) + scale_y_discrete("", expand = c(0, 0)) + 
    scale_fill_gradient2(name = "New Cases 000'", low = "#006400", mid = "#f2f6c3", 
        high = "#cd0000", midpoint = 0.5, na.value = "white") + theme(legend.position = "right", 
    axis.ticks = element_blank(), axis.text.x = element_text(angle = 90, hjust = 0.5), 
    axis.text.y = element_text(size = 10), panel.background = element_blank(), plot.title = element_text(size = 16, 
        face = "bold", color = "#0B8389"), plot.subtitle = element_text(size = 11))

new_data_agg <- data_agg[order(-data_agg$total_cases), ]
new_data_agg$total_cases_mln <- as.numeric(new_data_agg$total_cases/1e+06)
new_data_agg <- new_data_agg[1:15, ]
ggplot(data = new_data_agg, aes(x = total_cases_mln, y = reorder(location, total_cases_mln), 
    fill = continent)) + geom_bar(width = 0.8, stat = "identity") + labs(title = "Which are top 10 countries by Total Cases?", 
    subtitle = "USA, India & Brazil combines 45% of World's Total Cases", caption = "Date: 2021-Jan-29") + 
    xlab("Total Cases [mln]") + ylab("Countries") + theme(legend.position = "right", 
    text = element_text(size = 12), axis.text.y = element_text(hjust = 1), plot.caption = element_text(face = "italic", 
        size = 8), plot.title = element_text(size = 16, face = "bold", color = "#0B8389"), 
    plot.subtitle = element_text(size = 11)) + scale_fill_discrete(name = "Continent") + 
    geom_text(aes(label = round(total_cases_mln, 3)), vjust = 0.5, hjust = -0.03, 
        color = "darkgreen", size = 3.5) + scale_fill_brewer(palette = "Paired")

library(ggiraph)
library(ggplot2)
library(ggrepel)
# Basic plot:
data_agg_n <- data_agg %>% filter(gdp_per_capita > 10 & total_cases_per_million > 
    10)

g <- ggplot(data_agg_n, aes(x = gdp_per_capita, y = total_cases_per_million, color = continent)) + 
    geom_text_repel(data = subset(data_agg_n, gdp_per_capita > 72000), aes(label = location), 
        size = 5, box.padding = unit(0.35, "lines"), point.padding = unit(0.3, "lines"), 
        nudge_x = 0.8, nudge_y = 1.5, direction = "y", hjust = "left", segment.curvature = -0.1, 
        segment.ncp = 3, segment.angle = 20) + geom_point() + labs(title = "How is covid situation in rich countries?", 
    subtitle = "Europe cluster on the right-top while Africa cluster on the left bottom", 
    caption = "Date: 2021-Jan-29") + scale_x_continuous(trans = "log10", expand = expansion(mult = 0.5), 
    labels = comma) + scale_y_continuous(trans = "log10", labels = comma) + theme(legend.position = "bottom", 
    text = element_text(size = 12), plot.caption = element_text(face = "italic", 
        size = 8), plot.title = element_text(size = 16, face = "bold", color = "#0B8389"), 
    plot.subtitle = element_text(size = 11)) + coord_cartesian(clip = "off") + guides(color = guide_legend(override.aes = list(size = 6)))

# Interactiveness:
g_int <- g + geom_point_interactive(aes(tooltip = location), size = 3)

# Wyswietlenie
ggiraph(code = print(g_int))

# geom_label_repel(aes(gdp_per_capita, total_cases_per_million, fill=continent,
# label = location))

ggplot(data_agg, aes(x = gdp_per_capita, fill = continent)) + geom_histogram(data = data_agg[, 
    -5], alpha = 0.5, bins = 30, colour = "black") + labs(title = "Which continents have similar distribution of GDP_per_capita?", 
    subtitle = "Africa and Asia very much right-skewed", caption = "Date: 2021-Jan-29") + 
    facet_wrap(~continent) + guides(fill = FALSE) + theme(axis.text.x = element_text(colour = "grey20", 
    size = 10, angle = 90, hjust = 0.5, vjust = 0.5), axis.text.y = element_text(colour = "grey20", 
    size = 10), text = element_text(size = 12), plot.caption = element_text(face = "italic", 
    size = 8), plot.title = element_text(size = 16, face = "bold", color = "#0B8389"), 
    plot.subtitle = element_text(size = 11)) + scale_y_continuous(labels = comma) + 
    scale_x_continuous(labels = comma)

# ggplotly(b)

data_sel <- data.frame(data) %>% dplyr::select(continent, location, date, new_cases, 
    new_deaths, total_cases, total_deaths, total_cases_per_million, population)

knitr::kable(data_sel[1:5, ])

# data_anim <- data_sel %>% filter(location %in% c('Germany','Canada', 'Mexico',
# 'Italy', 'Spain', 'Poland'))

data_anim <- data_sel %>% filter(continent %in% c("Africa", "Asia", "Europe", "North America", 
    "South America", "Oceania"))
data_anim <- data_anim[complete.cases(data_anim), ]
gifplot <- ggplot(data_anim, aes(total_cases, total_deaths, size = population, colour = continent)) + 
    geom_point(alpha = 0.7, show.legend = FALSE) + scale_size(range = c(2, 12)) + 
    scale_x_log10() + facet_wrap(~continent) + # Here comes the gganimate specific bits
labs(title = "How virus spread in each continent in 2020?", subtitle = "Year: {frame_time}", 
    x = "Total Cases", y = "Total Deaths") + transition_time(date) + ease_aes("linear") + 
    shadow_wake(wake_length = 0.1, alpha = FALSE) + shadow_mark(alpha = 0.3, size = 0.5) + 
    theme(text = element_text(size = 12), plot.title = element_text(size = 16, face = "bold", 
        color = "#0B8389"), plot.subtitle = element_text(size = 14))


gganimate::animate(gifplot, duration = 15, fps = 20, renderer = gifski_renderer())
anim_save("gifplot.gif")

library(tidyverse)
library(rnaturalearth)
library(cowplot)
library(sf)
library(ggmap)
library(leaflet)
library("rnaturalearth")
library("rnaturalearthdata")
library("sf")
library("rgeos")
library(tidyverse)
library(ggplot2)
library(readr)
library(maps)
library(viridis)
library(plotly)

theme_set(theme_bw())

world <- ne_countries(scale = "medium", returnclass = "sf")
world <- data.frame(world)
world <- world %>% dplyr::rename(location = name)

worldmap <- world %>% dplyr::select(location, adm0_a3)
worldmap1 <- merge(x = worldmap, y = data_agg, by = "location", all.x = TRUE)
fig <- plot_ly(worldmap1, type = "choropleth", locations = worldmap1$adm0_a3, z = worldmap1$gdp_per_capita, 
    colors = "PuBuGn", hoverinfo = "text", text = ~paste("</br> Country: ", worldmap1$location, 
        "</br> GDP_per_capita: ", round(worldmap1$gdp_per_capita, 0), "</br> Total Cases: ", 
        worldmap1$total_cases, "</br> Cases per mln: ", round(worldmap1$total_cases_per_million, 
            3), "</br> Population mln: ", round(worldmap1$population_mln, 3))) %>% 
    layout(title = "All information about Countries, coloured according to GDP_per_capita", 
        size = 16, face = "bold", color = "#0B8389", legend = list(title = list(text = "<b> GDP_per_capita </b>"), 
            orientation = "h"))

fig

# library(htmlwidgets)

# saveWidget(fig, 'index.html')

library(ggplot2)
library(ggcorrplot)
library(tidyverse)
library(lubridate)
library(ggplot2)
library(readxl)
library(gganimate)
library(ggthemes)
library(MASS)
library(reshape2)
library(reshape)
library(DescTools)
library(dplyr)
library(stats)
options(scipen = 999)


exchange_rate_euro <- read.csv("eurofxref-hist.csv", stringsAsFactors = FALSE)
exchange_rate_euro <- exchange_rate_euro[, c(1:42)]
exchange_rate_euro[, c(2:42)] <- lapply(exchange_rate_euro[, c(2:42)], as.numeric)
exchange_rate_euro[is.na(exchange_rate_euro)] = 0

exchange_rate_euro[, 1] <- as.Date(exchange_rate_euro[, 1], "%Y-%m-%d")
exchange_rate_euro <- exchange_rate_euro %>% filter(Date >= as.Date("2020-01-01"))
df2 <- melt(exchange_rate_euro, id = c("Date"))
colnames(df2)[2:3] <- c("Currency", "Exchange_rate")
df <- df2[df2$Currency %in% c("USD"), ]
head(df)

        Date Currency Exchange_rate
1 2021-01-21      USD        1.2158
2 2021-01-20      USD        1.2101
3 2021-01-19      USD        1.2132
4 2021-01-18      USD        1.2064
5 2021-01-15      USD        1.2123
6 2021-01-14      USD        1.2124

currency_vs_country <- read.csv("tableconvert_csv_9gbdx9.csv")
colnames(currency_vs_country)[1] <- "Country"
temp1 <- merge(x = data_sel, y = currency_vs_country, by.x = "location", by.y = "Country", 
    all.x = TRUE)
temp2 <- merge(x = temp1, y = df2, by.x = c("Code", "date"), by.y = c("Currency", 
    "Date"), all.x = TRUE)
temp2 <- temp2[complete.cases(temp2), ]
temp2 <- temp2[temp2$Exchange_rate < 100, ]


temp3 <- temp2 %>% group_by(date, continent) %>% dplyr::summarize(Mean_ex = mean(Exchange_rate, 
    na.rm = TRUE), cases_pm = sum(new_cases)/max(population))
# temp4 <- melt(temp3, measure.vars =c('Mean_ex', 'Mean_ex'))
data_sub2 <- temp3 %>% filter(continent %in% c("Africa", "Asia", "Europe", "North America", 
    "South America", "Oceania"))
# data_sub2 <- temp3 %>% filter(continent %in% c( 'Europe'))

# data_sub2 <- data_sub2[data_sub2$Mean < 100,]

head(data_sub2)

# A tibble: 6 x 4
# Groups:   date [6]
  date       continent Mean_ex     cases_pm
  <date>     <chr>       <dbl>        <dbl>
1 2020-01-23 Asia         7.69 0.0000000660
2 2020-01-24 Asia         7.65 0.000000192 
3 2020-01-27 Asia         7.65 0.000000557 
4 2020-01-28 Asia         7.63 0.00000183  
5 2020-01-29 Asia         7.63 0.000000402 
6 2020-01-30 Asia         7.65 0.00000143  

library(hrbrthemes)
library(viridis)
library(ggplot2)
library(gganimate)
library(babynames)
library(ggrepel)

plot1 <- data_sub2 %>% ggplot(aes(x = date, y = Mean_ex, group = continent, color = continent)) + 
    geom_line() + geom_point() + geom_label_repel(aes(label = continent), nudge_x = 1, 
    na.rm = TRUE) + scale_color_viridis(discrete = TRUE) + labs(title = "Exchange Rate Trend by Continent", 
    x = "Date", y = "Exchange Rate") + theme(legend.position = "none", text = element_text(size = 12), 
    plot.title = element_text(size = 16, face = "bold", color = "#0B8389")) + transition_reveal(date)
plot1

anim_save("plot1.gif")

library(ggrepel)

plot2 <- data_sub2 %>% ggplot(aes(x = date, y = cases_pm, group = continent, color = continent), 
    show.Legend = FALSE) + geom_line() + geom_point() + geom_label_repel(aes(label = continent), 
    nudge_x = 1, na.rm = TRUE) + scale_color_viridis(discrete = TRUE) + labs(title = "Covid Cases per Capita Trend", 
    x = "Date", y = "Covid Cases per Capita") + theme(legend.position = "none", text = element_text(size = 12), 
    plot.title = element_text(size = 16, face = "bold", color = "#0B8389")) + transition_reveal(date)


gganimate::animate(plot2, duration = 20, fps = 20, renderer = gifski_renderer())

anim_save("plot2.gif")

options(width = 800)
library(treemap)
library(htmlwidgets)
# devtools::install_github('timelyportfolio/d3treeR')
library(d3treeR)

tree_df <- temp2 %>% group_by(continent, location) %>% mutate(Norm = Exchange_rate/max(Exchange_rate)) %>% 
    dplyr::select(continent, location, Norm)
tree_df <- data.frame(tree_df)

World <- treemap(tree_df, index = c("continent", "location", "Norm"), vSize = "Norm", 
    type = "index", palette = "Set3", bg.labels = c("white"), align.labels = list(c("center", 
        "center"), c("right", "bottom")))

# make it interactive ('rootname' becomes the title of the plot):
inter <- d3tree3(World)

# save the widget library(htmlwidgets)
saveWidget(inter, file = paste0(getwd(), "/interactiveTreemap.html"))

# library(broom.mixed)
library(jtools)
library(arm)
library(dplyr)


dat <- data[, c("continent", "date", "location", "total_cases_per_million", 
    "population", "gdp_per_capita", "stringency_index", "median_age", 
    "human_development_index")]

join1 <- merge(x = dat, y = currency_vs_country, by.x = "location", 
    by.y = "Country", all.x = TRUE)
join2 <- merge(x = join1, y = df2, by.x = c("Code", "date"), 
    by.y = c("Currency", "Date"), all.x = TRUE)

join2 <- join2[complete.cases(join2), ]
head(join2)

     Code       date location continent total_cases_per_million population gdp_per_capita stringency_index median_age human_development_index CountryCode Currency Exchange_rate
3323  BGN 2020-03-09 Bulgaria    Europe                   0.576    6948445       18563.31            21.30       44.7                   0.813          BG      Lev        1.9558
3324  BGN 2020-03-10 Bulgaria    Europe                   0.576    6948445       18563.31            21.30       44.7                   0.813          BG      Lev        1.9558
3325  BGN 2020-03-11 Bulgaria    Europe                   1.007    6948445       18563.31            26.85       44.7                   0.813          BG      Lev        1.9558
3326  BGN 2020-03-12 Bulgaria    Europe                   1.007    6948445       18563.31            26.85       44.7                   0.813          BG      Lev        1.9558
3327  BGN 2020-03-13 Bulgaria    Europe                   3.310    6948445       18563.31            50.93       44.7                   0.813          BG      Lev        1.9558
 [ reached 'max' / getOption("max.print") -- omitted 1 rows ]

join2 <- join2 %>% group_by(continent, location) %>% mutate(Norm = Exchange_rate/max(Exchange_rate))
reg_df <- join2 %>% group_by(continent, location) %>% mutate(Norm_cases = total_cases_per_million/max(total_cases_per_million))
reg_df <- reg_df[, !(colnames(reg_df) %in% c("CountryCode", "Code", 
    "location", "total_cases_per_million", "date"))]
reg_df <- na.omit(reg_df)
# reg_df$date<-as.character(reg_df$date)

# reg_df <- reg_df [,c('date','location', 'continent', 'Norm','Norm_cases')]
head(reg_df, 30)

# A tibble: 30 x 10
# Groups:   continent [1]
   continent population gdp_per_capita stringency_index median_age human_development_index Currency Exchange_rate  Norm Norm_cases
   <chr>          <dbl>          <dbl>            <dbl>      <dbl>                   <dbl> <chr>            <dbl> <dbl>      <dbl>
 1 Europe       6948445         18563.             21.3       44.7                   0.813 Lev               1.96     1  0.0000189
 2 Europe       6948445         18563.             21.3       44.7                   0.813 Lev               1.96     1  0.0000189
 3 Europe       6948445         18563.             26.8       44.7                   0.813 Lev               1.96     1  0.0000331
 4 Europe       6948445         18563.             26.8       44.7                   0.813 Lev               1.96     1  0.0000331
 5 Europe       6948445         18563.             50.9       44.7                   0.813 Lev               1.96     1  0.000109 
 6 Europe       6948445         18563.             50.9       44.7                   0.813 Lev               1.96     1  0.000246 
 7 Europe       6948445         18563.             56.5       44.7                   0.813 Lev               1.96     1  0.000317 
 8 Europe       6948445         18563.             70.4       44.7                   0.813 Lev               1.96     1  0.000435 
 9 Europe       6948445         18563.             70.4       44.7                   0.813 Lev               1.96     1  0.000444 
10 Europe       6948445         18563.             70.4       44.7                   0.813 Lev               1.96     1  0.000600 
# ... with 20 more rows

library(moonBook)
library(jtools)



Reg2 <- lm(formula = Norm ~ Norm_cases + continent, data = reg_df, 
    intercept = FALSE)
# Reg2$pred
summ(Reg2, exp = TRUE)

MODEL INFO:
Observations: 6360
Dependent Variable: Norm
Type: OLS linear regression 

MODEL FIT:
F(6,6353) = 176.72, p = 0.00
R² = 0.14
Adj. R² = 0.14 

Standard errors: OLS
-----------------------------------------------------------
                                Est.   S.E.   t val.      p
---------------------------- ------- ------ -------- ------
(Intercept)                     0.91   0.00   313.03   0.00
Norm_cases                      0.03   0.00    19.12   0.00
continentAsia                   0.02   0.00     5.78   0.00
continentEurope                 0.04   0.00    14.15   0.00
continentNorth America          0.02   0.00     6.35   0.00
continentOceania               -0.00   0.00    -1.01   0.31
continentSouth America         -0.02   0.00    -5.02   0.00
-----------------------------------------------------------

check <- data.frame(summary(Reg2)$coef[summary(Reg2)$coef[, 4] <= 
    0.001, 4])
check <- cbind(Variables = rownames(check), check)
rownames(check) <- 1:nrow(check)
colnames(check)[2] <- "P_Value"
check <- na.omit(check)
check <- check[order(check$P_Value), ]
# heck$P_Value <- round(check$P_Value,digits = 3)




p <- ggplot(Reg2, aes_string(x = names(Reg2$model)[2], y = names(Reg2$model)[3], 
    color = names(Reg2$model)[1])) + geom_col() + scale_fill_distiller(palette = "Reds", 
    direction = 1) + guides(col = guide_legend("Exchange Rate")) + 
    ggtitle("How does Exchange Rate differ in a Continent with given no. of Covid Cases?") + 
    # geom_text(aes(label=formatC(P_Value, format = 'f', digits =7))) +
theme_minimal() + xlab("Covid Cases") + ylab("Continent") + coord_flip() + 
    theme(panel.grid = element_blank(), panel.grid.major.y = element_line(color = "white"), 
        panel.ontop = TRUE)

p + transition_states(continent, wrap = FALSE) + shadow_mark() + 
    enter_grow() + enter_fade()

anim_save("plot3.gif")

library(sandwich)
# plot_summs(Reg)
ggplotly(effect_plot(Reg2, pred = Norm_cases, interval = TRUE, 
    colors = "purple", x.label = "Covid Cases", y.label = "Exchange rate", 
    robust = "HC0", main.title = "Actuals versus Predicted"))

ggplotRegression <- function(Reg) {
    
    require(ggplot2)
    require(ggthemes)
    
    ggplot(Reg$model, aes_string(x = names(Reg$model)[2], y = names(Reg$model)[1], 
        color = names(Reg$model)[3])) + geom_point() + ggtitle("Fit of the model") + 
        theme(plot.title = element_text(hjust = 0.5)) + xlab("Covid Cases") + 
        ylab("Exchange Rate") + guides(col = guide_legend("Continents")) + 
        stat_smooth(method = "lm", col = "red") + labs(subtitle = paste("Adj R2 = ", 
        signif(summary(Reg)$adj.r.squared, 5), "Intercept =", 
        signif(Reg$coef[[1]], 5), " Slope =", signif(Reg$coef[[2]], 
            5), " P =", round(summary(Reg)$coef[2, 4], 2)))
}
ggplotRegression(Reg2)